Find read files in a given directory.

find_read_files(directory, pattern = illumina_pattern,
  annotations = illumina_annotations, dirs_are_runs = FALSE)

Arguments

directory

The directory in which to look.

pattern

Regular expression pattern for the file names. Each capture group will be used as an annotation.

annotations

Names for the annotations. Must contain one name for each capture group in `pattern`.

dirs_are_runs

Whether subdirctories indicate different sequencing runs.

Value

A data table that contains the samples and their annotations.